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(v3.0.1.9059) Fix WISCA in vignette

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dr. M.S. (Matthijs) Berends
2026-06-23 14:38:59 +02:00
parent 3f9f931777
commit 9898b5df4b
41 changed files with 1310 additions and 757 deletions
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72
man/proportion.Rd
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@@ -15,40 +15,62 @@
\alias{sir_df}
\title{Calculate Antimicrobial Resistance}
\usage{
resistance(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE, guideline = getOption("AMR_guideline",
"EUCAST"))
resistance(
...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE,
guideline = getOption("AMR_guideline", "EUCAST")
)
susceptibility(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE, guideline = getOption("AMR_guideline",
"EUCAST"))
susceptibility(
...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE,
guideline = getOption("AMR_guideline", "EUCAST")
)
sir_confidence_interval(..., ab_result = "R", minimum = 30,
as_percent = FALSE, only_all_tested = FALSE, confidence_level = 0.95,
side = "both", collapse = FALSE)
sir_confidence_interval(
...,
ab_result = "R",
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE,
confidence_level = 0.95,
side = "both",
collapse = FALSE
)
proportion_R(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
proportion_R(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)
proportion_IR(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
proportion_IR(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)
proportion_I(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
proportion_I(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)
proportion_SI(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
proportion_SI(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)
proportion_S(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
proportion_S(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)
proportion_df(data, translate_ab = "name", language = get_AMR_locale(),
minimum = 30, as_percent = FALSE, combine_SI = TRUE,
confidence_level = 0.95)
proportion_df(
data,
translate_ab = "name",
language = get_AMR_locale(),
minimum = 30,
as_percent = FALSE,
combine_SI = TRUE,
confidence_level = 0.95
)
sir_df(data, translate_ab = "name", language = get_AMR_locale(),
minimum = 30, as_percent = FALSE, combine_SI = TRUE,
confidence_level = 0.95)
sir_df(
data,
translate_ab = "name",
language = get_AMR_locale(),
minimum = 30,
as_percent = FALSE,
combine_SI = TRUE,
confidence_level = 0.95
)
}
\arguments{
\item{...}{One or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link[=as.sir]{as.sir()}} if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See \emph{Examples}.}